Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/test/Test_F_WrappGetLetterDistribution.py @ 6:769e306b7933
Change the repository level.
| author | yufei-luo |
|---|---|
| date | Fri, 18 Jan 2013 04:54:14 -0500 |
| parents | |
| children |
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| 5:ea3082881bf8 | 6:769e306b7933 |
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| 1 import unittest | |
| 2 import os | |
| 3 from commons.core.utils.FileUtils import FileUtils | |
| 4 from SMART.galaxy.WrappGetLetterDistribution import WrappGetLetterDistribution | |
| 5 | |
| 6 SMART_PATH = "%s/SMART" % os.environ["REPET_PATH"] | |
| 7 SMART_DATA = SMART_PATH + "/data" | |
| 8 | |
| 9 class Test_F_WrappGetLetterDistribution(unittest.TestCase): | |
| 10 | |
| 11 | |
| 12 def setUp(self): | |
| 13 self._dirTest = "%s/galaxy/test" % SMART_PATH | |
| 14 self._iwrappFastq = WrappGetLetterDistribution() | |
| 15 self._iwrappFasta = WrappGetLetterDistribution() | |
| 16 self._expOutputCSV = "expOutputTomate.csv" | |
| 17 | |
| 18 def test_wrappFasta(self): | |
| 19 self._iwrappFasta._inputFileName = "%s/SR1.fasta" % SMART_DATA | |
| 20 self._iwrappFasta._outputFileNamePrefix = "%s/galaxy/test/TomateFasta_res" % SMART_PATH | |
| 21 self._iwrappFasta._outputFileNamePNG = "%s/galaxy/test/TomateFasta_res.png" % SMART_PATH | |
| 22 self._iwrappFasta._outputFileNamePerNtPNG = "%s/galaxy/test/TomateFasta_resPerNt.png" % SMART_PATH | |
| 23 self._iwrappFasta._outputFileNameCSV = "%s/galaxy/test/TomateFasta_res.csv" % SMART_PATH | |
| 24 self._iwrappFasta._inputFileFormat = "fasta" | |
| 25 self._iwrappFasta._csv = True | |
| 26 if not(FileUtils.isEmpty(self._iwrappFasta._inputFileName)): | |
| 27 self._iwrappFasta.wrapp() | |
| 28 self.assertTrue(os.path.exists(self._iwrappFasta._outputFileNamePNG)) | |
| 29 self.assertTrue (os.path.exists(self._iwrappFasta._outputFileNamePerNtPNG)) | |
| 30 self.assertTrue (os.path.exists(self._iwrappFasta._outputFileNameCSV)) | |
| 31 self.assertTrue(FileUtils.are2FilesIdentical(self._iwrappFasta._outputFileNameCSV,self._expOutputCSV)) | |
| 32 else: | |
| 33 print "Problem : the input fasta file %s is empty!" % self._inputFileFasta | |
| 34 | |
| 35 | |
| 36 # def test_wrappFasta_withoutCSV_Opt(self): | |
| 37 # self._iwrappFasta._inputFileName = "%s/SR1.fasta" % SMART_DATA | |
| 38 # self._iwrappFasta._outputFileNamePrefix = "%s/galaxy/test/TomateFasta_res" % SMART_PATH | |
| 39 # self._iwrappFasta._outputFileNamePNG = "%s/galaxy/test/TomateFasta_res.png" % SMART_PATH | |
| 40 # self._iwrappFasta._outputFileNamePerNtPNG = "%s/galaxy/test/TomateFasta_resPerNt.png" % SMART_PATH | |
| 41 # self._iwrappFasta._outputFileNameCSV = "%s/galaxy/test/TomateFasta_res.csv" % SMART_PATH | |
| 42 # self._iwrappFasta._inputFileFormat = "fasta" | |
| 43 # self._iwrappFasta._csv = False | |
| 44 # if not(FileUtils.isEmpty(self._iwrappFasta._inputFileName)): | |
| 45 # self._iwrappFasta.wrapp() | |
| 46 # self.assertTrue(os.path.exists(self._iwrappFasta._outputFileNamePNG)) | |
| 47 # self.assertTrue (os.path.exists(self._iwrappFasta._outputFileNamePerNtPNG)) | |
| 48 # else: | |
| 49 # print "Problem : the input fasta file %s is empty!" % self._inputFileFasta | |
| 50 # os.system("rm %s/galaxy/test/*_res*.png" %SMART_PATH) | |
| 51 # os.system("rm %s/galaxy/test/*_res.csv" %SMART_PATH) | |
| 52 # | |
| 53 # | |
| 54 # def test_wrappFastq(self): | |
| 55 # self._iwrappFastq._inputFileName = "%s/SR1.fastq" % SMART_DATA | |
| 56 # self._iwrappFastq._outputFileNamePrefix = "%s/galaxy/test/TomateFastq_res" % SMART_PATH | |
| 57 # self._iwrappFastq._outputFileNamePNG = "%s/galaxy/test/TomateFastq_res.png" % SMART_PATH | |
| 58 # self._iwrappFastq._outputFileNamePerNtPNG = "%s/galaxy/test/TomateFastq_resPerNt.png" % SMART_PATH | |
| 59 # self._iwrappFastq._outputFileNameCSV = "%s/galaxy/test/TomateFastq_res.csv" % SMART_PATH | |
| 60 # self._iwrappFastq._inputFileFormat = "fastq" | |
| 61 # self._iwrappFastq._csv = True | |
| 62 # if not(FileUtils.isEmpty(self._iwrappFastq._inputFileName)): | |
| 63 # self._iwrappFastq.wrapp() | |
| 64 # self.assertTrue(os.path.exists(self._iwrappFastq._outputFileNamePNG)) | |
| 65 # self.assertTrue (os.path.exists(self._iwrappFastq._outputFileNamePerNtPNG)) | |
| 66 # self.assertTrue (os.path.exists(self._iwrappFastq._outputFileNameCSV)) | |
| 67 # self.assertTrue(FileUtils.are2FilesIdentical(self._iwrappFastq._outputFileNameCSV,self._expOutputCSV)) | |
| 68 # else: | |
| 69 # print "Problem : the input fastq file %s is empty!" % self._inputFileFastq | |
| 70 # | |
| 71 # | |
| 72 # def test_wrappFastq_withoutCSV_Opt(self): | |
| 73 # self._iwrappFastq._inputFileName = "%s/SR1.fastq" % SMART_DATA | |
| 74 # self._iwrappFastq._outputFileNamePrefix = "%s/galaxy/test/TomateFastq_res" % SMART_PATH | |
| 75 # self._iwrappFastq._outputFileNamePNG = "%s/galaxy/test/TomateFastq_res.png" % SMART_PATH | |
| 76 # self._iwrappFastq._outputFileNamePerNtPNG = "%s/galaxy/test/TomateFastq_resPerNt.png" % SMART_PATH | |
| 77 # self._iwrappFastq._outputFileNameCSV = "%s/galaxy/test/TomateFastq_res.csv" % SMART_PATH | |
| 78 # self._iwrappFastq._inputFileFormat = "fastq" | |
| 79 # self._iwrappFastq._csv = False | |
| 80 # if not(FileUtils.isEmpty(self._iwrappFastq._inputFileName)): | |
| 81 # self._iwrappFastq.wrapp() | |
| 82 # self.assertTrue(os.path.exists(self._iwrappFastq._outputFileNamePNG)) | |
| 83 # self.assertTrue (os.path.exists(self._iwrappFastq._outputFileNamePerNtPNG)) | |
| 84 # else: | |
| 85 # print "Problem : the input fastq file %s is empty!" % self._inputFileFastq | |
| 86 # os.system("rm %s/galaxy/test/*_res*.png" %SMART_PATH) | |
| 87 # os.system("rm %s/galaxy/test/*_res.csv" %SMART_PATH) | |
| 88 | |
| 89 | |
| 90 if __name__ == "__main__": | |
| 91 unittest.main() |